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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%",
warning = FALSE,
message = FALSE
)
```
# subpat
<!-- badges: start -->
[![Travis build status](https://travis-ci.org/Novartis/subpat.svg?branch=master)](https://travis-ci.org/Novartis/subpat)
<!-- badges: end -->
[![lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://img.shields.io/badge/lifecycle-experimental-orange.svg)
> This package is NOT VALIDATED, and should be reserved for exploratory analysis only.
subpat is a collection of shiny modules to create subpopulations and subgroups of clinical trial data.
It was designed with [CDISC ADaM](https://www.cdisc.org/standards/foundational/adam) data format in mind but supports any data format. It features two main applications, the Patient Listing Generator (PLG), and a TTE (time-to-event) analysis app.
## Install
subpat is not available on CRAN. A development version can be installed by running
```{r, eval = F}
devtools::install_github("Novartis/subpat")
```
## Patient Listing Generator (PLG)
PLG is designed for non-techincal users such as medical writers or clinicians to find specific patients and generate ad-hoc listings.
It features an intuitive, graphical patient querying interface to find specific subjects from a clinical trial.
The user can then use the created subpopulation to create ad-hoc (non-validated) listing to export.
All of the components of the application can easily be reused in other Shiny applications due to the modular design.
## TTE (time-to-event) analysis
The time-to-event (TTE) analysis application is a graphical and exploratory way for a statistician to analyze censored event data (such as survival times).
This app uses the same subpopulation module as the PLG as well as a similarly designed subgroup creation interface.
The subpopulations and subgroups are then used in the Kaplan Meier plots and Cox Proportional model modules.
The variables are easily mapped to allow for data in any format.
## Modules
It features modules for:
- Subpopulation creation and editing
- Subgroup creation and editing
- Ad-hoc patient listings
- Kaplan Meier survival plots and event table summary
- Cox Proportional Hazard models
All of these modules are implemented with the [`{tidymodules}`](https://opensource.nibr.com/tidymodules) R package.
## Usage
### Patient Listing Generator (PLG)
```{r, eval = F}
subpat::runPlg()
```
### TTE Analysis
```{r, eval = F}
subpat::runTTE()
```
### Modules
subpat features many example Shiny applications to get you started using the modules.
To see a list of examples, run
```{r}
subpat::subpatExamples()
```
All of the examples are found in [inst/shiny-examples](inst/shiny-examples).
## Vignettes
A more detailed introduction is found in the vignettes
### PLG
```{r, eval = F}
vignette("plg", package = "subpat")
```
### Modules Introduction
```{r, eval = F}
vignette("modules", package = "subpat")
```
### TTE Module Integration
```{r, eval = F}
vignette("tte_integration.Rmd", package = "subpat")
```
## Thanks
Special thanks to the SCC team at Novartis
- Mustapha Larbaoui [\@m-l-1](https://github.com/m-l-1)
- Xiao Ni [\@xni7](https://github.com/xni7)
- David Granjon [\@DivadNojnarg](https://github.com/DivadNojnarg)
- Douglas Robinson
- Renan Sauteraud [\@SRenan](https://github.com/SRenan)
- Marzie Rasekh [\@marzie-rasekh](https://github.com/marzie-rasekh)
Also thanks to Novartis for allowing this work to become an open-source project. It was started during my summer 2019 internship in Basel.
## License
Copyright 2020 Novartis AG
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.